The HistologyImaging - Class

S4 class that represents a set of histological images from one and the same tissue slide.

Slots

annotations

list. List of objects of class ImageAnnotation.

coordinates

data.frame. A data.frame of observational units that underlie the image in case of spatially resolved multi-omic studies. Should contain at least the two variables: x, y and a variable that identifies the observational units (e.g. barcodes).

dir_add

list. Named list of directories that contain different versions of tissue images. Can be arbitrarily expanded for convenient exchanging via loadImage().

dir_default

character. Directory that leads to the default image for save exchanging via loadDefaultImage().

dir_highres

character. Directory that leads to a high resolution version of the image for save exchanging via loadHighresImage().

dir_lowres

character. Directory that leads to a low resolution version of the image for save exchanging via loadLowresImage().

grid

list. That contains information about spatial grids.

id

character. String to identify the imaged tissue.

image

Image. Should be compatible with the EBImage package.

image_info

list. Stores meta data and miscellaneous information regarding the image that is currently stored in slot @image. Slots that should always exist:

  • origin: Character string. Either the directory from where the current image was read in or a substitute of the object name that was used from the global environment.

  • dim_input: The dimensions with which the image was given to argument image of createHistologyImaging() or exchangeImage().

  • dim_stored: The dimensions with which the image is currently stored.

  • img_scale_fct: The scale factor input that was used to resize the current image within createHistologyImaging() or exchangeImage() before setting it. If 1, dim_stored and dim_input should be identical. See argument scale_fct of exchangeImage() for more details on its interpretation.

  • pxl_scale_fct: Numeric value that gives the side length of one pixel an SI unit that is stated in an attribute called unit as nSI-units/px.

justification

list. List of two slots that track justification changes. See corresponding section below the slot descriptions for more information.

  • angle: Numeric value that ranges from 0-359.

  • flipped: List of two logical values named horizontal and vertical.

meta

list. List for meta data regarding the tissue.

misc

list. A flexible list for miscellaneous input.

Requirements

The HistologyImaging framework assumes that all read in images have the same axes-ratio.

Tracking changes in image justification

The histology image that is used while creating the object is considered the default image. By default, the framework assumes that all related images (high resolution, low resolution, fluorescent images, RAMAN spectroscopy etc.) have the same justification in terms of angle rotation and axes-flipping. Flipping an image in the SPATA2 object via flipImage() or rotating images via rotateImage() changes their justification in space. These changes in justification are tracked (if track is not set to FALSE) and applied whenever an image is exchanged via exchangeImage() (if adjust is not set to FALSE). This ensures consistent image exchanges using the different directories.